2. When you build your application and collective from the toplevel patch, make sure to include your actual patch and all its dependencies in the build script, because they will not be included automatically.

3. After you have built your application, use the technique found here

to prevent the menu bar and application icon on the dock from showing up.

What results is a program that is invisible to the user (aka does not have a menu bar, does not show up on the dock, does not show up as a process under force quit, and does not have a window). It is also impossible for the anything to end the process outside of a program, so you better have a way to stop it when you want it to. For instance, I am using this method to run max as an audio engine for Unity, and here is the C# code I use to start the program and end it (using System.Diagnostics and System.IO from the .Net library, included with Unity).